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Detailed information for vg0222557484:

Variant ID: vg0222557484 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22557484
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

CTGCAAGTAGATTTGAAGAAAGTCTCCATACTCCAACTTGCCTTGAACATGCAAGAATTAGGATGGCGGCGACTGAACCCCTGTCTTGTAACGATTTGGC[G/A]
GAGGTACGCAACACCGGAGATGGAAGGGAAAATGTTGCCGCAGAGAGCTTCAATAAGCAGGAGCCTGAGCAACCAACCAACAAGCTTGCCACCAAGAGCT

Reverse complement sequence

AGCTCTTGGTGGCAAGCTTGTTGGTTGGTTGCTCAGGCTCCTGCTTATTGAAGCTCTCTGCGGCAACATTTTCCCTTCCATCTCCGGTGTTGCGTACCTC[C/T]
GCCAAATCGTTACAAGACAGGGGTTCAGTCGCCGCCATCCTAATTCTTGCATGTTCAAGGCAAGTTGGAGTATGGAGACTTTCTTCAAATCTACTTGCAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.60%	46.20%	1.88%	1.25%	NA
All Indica	2759	78.10%	17.90%	2.61%	1.45%	NA
All Japonica	1512	1.80%	96.80%	0.33%	1.12%	NA
Aus	269	70.30%	27.90%	1.49%	0.37%	NA
Indica I	595	74.60%	18.80%	4.03%	2.52%	NA
Indica II	465	92.70%	5.80%	0.86%	0.65%	NA
Indica III	913	70.00%	25.30%	2.63%	2.08%	NA
Indica Intermediate	786	81.40%	15.60%	2.54%	0.38%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	4.20%	91.70%	0.79%	3.37%	NA
Japonica Intermediate	241	0.80%	98.80%	0.41%	0.00%	NA
VI/Aromatic	96	1.00%	92.70%	6.25%	0.00%	NA
Intermediate	90	24.40%	72.20%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0222557484	G -> A	LOC_Os02g37309.1	missense_variant ; p.Arg85Cys; MODERATE	nonsynonymous_codon ; R85C	Average:52.59; most accessible tissue: Callus, score: 80.626	unknown	unknown	TOLERATED	0.15
vg0222557484	G -> DEL	LOC_Os02g37309.1	N	frameshift_variant	Average:52.59; most accessible tissue: Callus, score: 80.626	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222557484	NA	2.82E-39	mr1124	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	NA	5.13E-08	mr1222	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	1.70E-07	4.40E-07	mr1913	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	8.78E-06	NA	mr1067_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	8.67E-08	NA	mr1067_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	NA	1.00E-37	mr1072_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	NA	3.79E-38	mr1075_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	NA	1.07E-23	mr1077_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	3.37E-06	NA	mr1124_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	NA	7.98E-12	mr1595_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	NA	2.08E-09	mr1600_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	NA	1.48E-06	mr1908_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	9.02E-06	NA	mr1918_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222557484	NA	3.42E-09	mr1947_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251